Dear Marek,
It looks like the atom is part of a ligand, with its prmtop file generated
by antechamber, I guess. Unfortunately, the nonpolar solvent model for
general organic molecules has yet been trained ... Neither radiopt=1 nor
radiopt=0 would work for ligand molecules ...
All the best,
Ray
On Tue, Mar 15, 2011 at 6:45 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Dear all,
>
> recently I wanted to do MM/PBSA analysis of my system using mm_pbsa.pl
> script (AmberTools 1.4)
> using INP=2 as it is recommended for case of branched and cyclic molecules
> in Amber manual.
> As recommended for this choice I also set RADIOPT=1.
>
> Unfortunately calculation crashed with this error:
>
>
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 616 C4 CG
>
>
> when I tried to use RADIOPT=0 to force reading atom radii from PRMTOP
> file, it crashed immediately
> with no error message written in any output file.
>
> It seems that RADIOPT=1 is really mandatory for INP=2.
>
>
> My interpretation of the above error is that Tan & Luo radius for Glycam
> atom type "CG" is
> unknown. If I am right I just don.t understand why in such case atom
> radius from PRMTOP file
> is not automatically used like in case of GAFF ( lowercase ) forcefield.
>
>
> I would be grateful for any useful advice here (To change all CG to CT in
> prmtop file (just for PB calculation) ? or to add some lines in relevant
> Amber source file ? ...).
>
> Thanks in advance !
>
> Best wishes,
>
> Marek
>
>
>
> Here is for completnes relevant part of my MM/PBSA input file:
>
> #
> # Input parameters for mm_pbsa.pl
> #
> # Holger Gohlke
> # 25.02.2010
> #
>
> ################################################################################
> .GENERAL
> #
> # General parameters
> # 0: means NO; >0: means YES
> #
> # mm_pbsa allows to calculate (absolute) free energies for one molecular
> # species or a free energy difference according to:
> #
> # Receptor + Ligand = Complex,
> # DeltaG = G(Complex) - G(Receptor) - G(Ligand).
> #
> # VERBOSE - If set to 1, input and output files are not removed. This is
> useful for
> # debugging purposes.
> # PARALLEL - If set to values > 1, energy calculations for snapshots are
> done
> # in parallel, using PARALLEL number of threads.
> #
> # PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during
> # generation of snapshots as well as during mm_pbsa
> calculations.
> # PATH - Specifies the location where to store or get snapshots.
> # START - Specifies the first snapshot to be used in energy calculations
> (optional, defaults to 1).
> # STOP - Specifies the last snapshot to be used in energy calculations
> (optional, defaults to 10e10).
> # OFFSET - Specifies the offset between snapshots in energy calculations
> (optional, defaults to 1).
> #
> # COMPLEX - Set to 1 if free energy difference is calculated.
> # RECEPTOR - Set to 1 if either (absolute) free energy or free energy
> # difference are calculated.
> # LIGAND - Set to 1 if free energy difference is calculated.
> #
> # COMPT - parmtop file for the complex (not necessary for option GC).
> # RECPT - parmtop file for the receptor (not necessary for option GC).
> # LIGPT - parmtop file for the ligand (not necessary for option GC).
> #
> # GC - Snapshots are generated from trajectories (see below).
> # AS - Residues are mutated during generation of snapshots from
> trajectories.
> # DC - Decompose the free energies into individual contributions
> # (only works with MM and GB).
> #
> # MM - Calculation of gas phase energies using sander.
> # GB - Calculation of desolvation free energies using the GB models in
> sander
> # (see below).
> # PB - Calculation of desolvation free energies using delphi (see below).
> # Calculation of nonpolar solvation free energies according to
> # the INP option in pbsa (see below).
> # MS - Calculation of nonpolar contributions to desolvation using molsurf
> # (see below).
> # If MS == 0 and GB == 1, nonpolar contributions are calculated
> with the
> # LCPO method in sander.
> # If MS == 0 and PB == 1, nonpolar contributions are calculated
> according
> # the INP option in pbsa (see below).
> # NM - Calculation of entropies with nmode.
> #
> VERBOSE 0
> PARALLEL 2
> #
> PREFIX snap
> PATH ../0_snaps
> START 399
> STOP 400
> OFFSET 1
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ../prmtop/com.prmtop
> RECPT ../prmtop/rec.prmtop
> LIGPT ../prmtop/lig.prmtop
> #
> GC 0
> AS 0
> DC 0
> #
> MM 1
> GB 0
> PB 1
> MS 0
> #
> NM 0
> #
>
> ################################################################################
> .PB
> #
> # PB parameters (this section is only relevant if PB = 1 above)
> #
> # The following parameters are passed to the PB solver.
> # Additional input parameters may also be added here. See the sander PB
> # documentation for more options.
> #
> # PROC - Determines which method is used for solving the PB equation:
> # By default, PROC = 2, the pbsa program of the AMBER suite is
> used.
> # REFE - Determines which reference state is taken for PB calc:
> # By default, REFE = 0, reaction field energy is calculated with
> # EXDI/INDI. Here, INDI must agree with DIELC from MM part.
> # INDI - Dielectric constant for the solute.
> # EXDI - Dielectric constant for the surrounding solvent.
> # ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.
> # PRBRAD - Solvent probe radius in Angstrom:
> # 1.4: with the radii in the prmtop files. Default.
> # 1.6: with the radii optimized by Tan and Luo (In preparation).
> # See RADIOPT on how to choose a cavity radii set.
> # RADIOPT - Option to set up radii for PB calc:
> # 0: uses the radii from the prmtop file. Default.
> # 1: uses the radii optimized by Tan and Luo (In preparation)
> # with respect to the reaction field energies computed
> # in the TIP3P explicit solvents. Note that optimized radii
> # are based on AMBER atom types (upper case) and charges.
> # Radii from the prmtop files are used if the atom types
> # are defined by antechamber (lower case).
> # SCALE - Lattice spacing in no. of grids per Angstrom.
> # LINIT - No. of iterations with linear PB equation.
> # IVCAP - If set to 1, a solvent sphere (specified by CUTCAP,XCAP,YCAP,
> # and ZCAP) is excised from a box of water. If set to 5, a
> solvent shell
> # is excised, specified by CUTCAP (the thickness of the shell in
> A).
> # The electrostatic part
> # of the solvation free energy is estimated from a linear
> response
> # approximation using the explicit water plus a reaction field
> # contribution from outside the sphere (i.e., a hybrid solvation
> approach
> # is pursued). In addition, the nonpolar
> # contribution is estimated from a sum of (attractive) dispersion
> # interactions calc. between the solute and the solvent molecules
> # plus a (repulsive) cavity contribution. For the latter,
> # the surface calculation must be done with MS = 1 and the PROBE
> should
> # be set to 1.4 to get the solvent excluded surface.
> # CUTCAP - Radius of the water sphere or thickness of the water shell.
> # Note that the sphere must enclose the whole solute.
> # XCAP - Location of the center of the water sphere.
> # YCAP
> # ZCAP
> #
> # NP Parameters for nonpolar solvation energies if MS = 0
> #
> # INP - Option for modeling nonpolar solvation free energy.
> # See sander PB documentation for more information on the
> # implementations by Tan and Luo (In preparation).
> # 1: uses the solvent-accessible-surface area to correlate total
> # nonpolar solvation free energy:
> # Gnp = SURFTEN * SASA + SURFOFF. Default.
> # 2: uses the solvent-accessible-surface area to correlate the
> # repulsive (cavity) term only, and uses a surface-integration
> # approach to compute the attractive (dispersion) term:
> # Gnp = Gdisp + Gcavity
> # = Gdisp + SURFTEN * SASA + SURFOFF.
> # When this option is used, RADIOPT has to be set to 1,
> # i.e. the radii set optimized by Tan and Luo to mimic Gnp
> # in TIP3P explicit solvents. Otherwise, there is no guarantee
> # that Gnp matches that in explicit solvents.
> # SURFTEN/SURFOFF - Values used to compute the nonpolar
> # solvation free energy Gnp acccording to INP.
> # If INP = 1 and RADIOPT = 0 (default, see above),
> # use SURFTEN/SURFOFF parameters that fit with the radii from the
> # prmtop file, e.g., use SURFTEN: 0.00542; SURFOFF: 0.92 for
> PARSE radii.
> # If INP = 2 and RADIOPT = 1, these two lines
> # can be removed, i.e. use the default values set in pbsa
> # for this nonpolar solvation model. Otherwise, please
> # set these to the following: SURFTEN: 0.04356; OFFSET: -1.008
> #
> # NP Parameters for nonpolar solvation energies if MS = 1
> #
> # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution Gnp
> to
> # the desolvation according to either
> # (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP = 0) or
> # (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA + SURFOFF
> (if IVCAP > 0).
> # In the case of (I), use parameters that fit with the radii
> from the
> # reaction field calculation. E.g., use SURFTEN: 0.00542,
> SURFOFF: 0.92
> # for PARSE radii or use SURFTEN: 0.005, SURFOFF: 0.86 for Tan &
> Luo radii.
> # In the case of (II), use SURFTEN: 0.069; SURFOFF: 0.00 for
> calculating the
> # Gcavity contribution.
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 3
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 1
> INP 2
> #
> #SURFTEN 0.00542
> #SURFOFF 0.92
> #
> IVCAP 0
> CUTCAP -1.0
> XCAP 0.0
> YCAP 0.0
> ZCAP 0.0
> #
>
> ################################################################################
>
>
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Received on Tue Mar 15 2011 - 22:00:03 PDT
